GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Williamsia sterculiae CPCC 203464

Best path

pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA

Rules

Overview: 4-hydroxybenzoate catabolism in GapMind is based on aerobic oxidation to 3,4-hydroxybenzoate (protocatechuate), followed by meta, ortho, or para cleavage; or reduction to benzoyl-CoA (part of a MetaCyc pathway for phenol degradation, link)

72 steps (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BW971_RS05790 BW971_RS18685
praC 2-hydroxymuconate tautomerase BW971_RS17575
praD 2-oxohex-3-enedioate decarboxylase BW971_RS01145
mhpD 2-hydroxypentadienoate hydratase BW971_RS01145
mhpE 4-hydroxy-2-oxovalerate aldolase BW971_RS01135
ald-dh-CoA acetaldehyde dehydrogenase, acylating BW971_RS01140 BW971_RS03540
Alternative steps:
ackA acetate kinase BW971_RS08540 BW971_RS01390
acs acetyl-CoA synthetase, AMP-forming BW971_RS08810 BW971_RS18805
adh acetaldehyde dehydrogenase (not acylating) BW971_RS18685 BW971_RS10750
atoB acetyl-CoA C-acetyltransferase BW971_RS20375 BW971_RS04170
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BW971_RS03935 BW971_RS10815
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BW971_RS02255 BW971_RS10800
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BW971_RS16050 BW971_RS12060
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BW971_RS00825
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit
bamG class II benzoyl-CoA reductase, BamG subunit
bamH class II benzoyl-CoA reductase, BamH subunit BW971_RS09375
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit
boxA benzoyl-CoA epoxidase, subunit A
boxB benzoyl-CoA epoxidase, subunit B
boxC 2,3-epoxybenzoyl-CoA dihydrolase
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase BW971_RS05230 BW971_RS19425
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BW971_RS16050 BW971_RS12060
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BW971_RS12060 BW971_RS00105
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BW971_RS08035 BW971_RS03020
fcbT1 tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1
fcbT2 tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2
fcbT3 tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3
gcdH glutaryl-CoA dehydrogenase BW971_RS08610 BW971_RS19425
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase BW971_RS16360 BW971_RS04860
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit BW971_RS05055
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit BW971_RS05055
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase
ligI 2-pyrone-4,6-dicarboxylate hydrolase
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase BW971_RS18570
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase BW971_RS12060 BW971_RS07840
paaH 3-hydroxyadipyl-CoA dehydrogenase BW971_RS08035 BW971_RS03020
paaJ2 3-oxoadipyl-CoA thiolase BW971_RS00100 BW971_RS04170
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase BW971_RS20300 BW971_RS20760
pcaD 3-oxoadipate enol-lactone hydrolase BW971_RS20760
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BW971_RS00100 BW971_RS04170
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BW971_RS04170 BW971_RS00100
pimC pimeloyl-CoA dehydrogenase, small subunit BW971_RS08290 BW971_RS09920
pimD pimeloyl-CoA dehydrogenase, large subunit BW971_RS08285 BW971_RS09925
pimF 6-carboxyhex-2-enoyl-CoA hydratase BW971_RS00105
pta phosphate acetyltransferase BW971_RS08545
xylF 2-hydroxymuconate semialdehyde hydrolase BW971_RS15160 BW971_RS01160

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory